FIGURE 5.
VapCRv0065 and VapCRv0617 target GC sequences. (A) MALDI-TOF MS of 932 RNA oligonucleotide three negative controls (RNA 0 and 60 min and EDTA) show no degradation of the RNA oligonucleotide due to ribonuclease contamination. Time course assays of VapCRv0065 and VapCRv0617 show optimal cut sites at GCC and GGG (indicated by red fragments in B). Other less optimal cut sites appear later in the time course (15–60 min; black fragments in B). (B) 932 RNA oligonucleotide three with corresponding cut sites and m/z values; dotted lines represent fragments that were below the MS detection limit. (C) Analysis of VapC cleavage sites across 932 RNA oligonucleotides as calculated by WebLogo (Crooks et al. 2004). VapC cleavage position indicated by arrow. The height of the letter is proportional to the frequency of that base at that particular position.